Entropy from state probabilities: Hydration entropy of cations

Journal of Physical Chemistry B

Volumn 117, Issue 21, 2013, Pages 6466-6472

  Huber, Roland G ^a   Fuchs, Julian E ^a   Von Grafenstein, Susanne ^a   Laner, Monika ^a,c   Wallnoefer, Hannes G ^a   Abdelkader, Nejma ^b   Kroemer, Romano T ^b   Liedl, Klaus R ^a  

^a UNIVERSITY OF INNSBRUCK   (Austria)

^b SANOFI   (France)

^c ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; HYDRATION; POSITIVE IONS; PROBABILITY DENSITY FUNCTION;

CHEMICAL PROCESS; CHEMICAL SYSTEMS; CONFORMATIONAL SPACE; HYDRATION ENTROPY; NANOSECOND RANGE; ORDER PARAMETER; POTENTIAL ENERGY LANDSCAPES; STATE PROBABILITY;

ENTROPY;

EID: 84878366230     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp311418q     Document Type: Article

References (45)

1. Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. The Statistical-Thermodynamic Basis for Computation of Binding Affinities: A Critical Review Biophys. J. 1997, 72, 1047-1069
2. Gilson, M. K.; Zhou, H.-X. Calculation of Protein-Ligand Binding Affinities Annu. Rev. Biophys. Biomol. Struct. 2007, 36, 21-42
3. Li, Z.; Lazaridis, T. Water at Biomolecular Binding Interfaces Phys. Chem. Chem. Phys. 2007, 9, 573-581
4. Freire, E. A Thermodynamic Approach to the Affinity Optimization of Drug Candidates Chem. Biol. Drug Des. 2009, 74, 468-472
5. Schoen, A.; Lam, S. Y.; Freire, E. Thermodynamics-Based Drug Design: Strategies for Inhibiting Protein-Protein Interactions Future Med. Chem. 2011, 3, 1129-1137
6. Abel, R.; Young, T.; Farid, R.; Berne, B. J.; Friesner, R. A. Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding J. Am. Chem. Soc. 2008, 130, 2817-2831
7. Wang, L.; Berne, B. J.; Friesner, R. A. Ligand Binding to Protein-Binding Pockets with Wet and Dry Regions Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 1326-1330
8. Irudayam, S. J.; Henchman, R. H. Entropic Cost of Protein-Ligand Binding and Its Dependence on the Entropy in Solution J. Phys. Chem. B 2009, 113, 5871-5884
9. Dinola, A.; Berendsen, H.; Edholm, O. Free-Energy Determination of Polypeptide Conformations Generated by Molecular Dynamics Macromolecules 1984, 17, 2044-2050
10. Karplus, M.; Kushick, J. Method for Estimating the Configurational Entropy of Macromolecules Macromolecules 1981, 14, 325-332
11. Ichiye, T.; Karplus, M. Collective Motions in Proteins-A Covariance Analysis of Atomic Fluctuations in Molecular Dynamics and Normal Mode Simulations Proteins 1991, 11, 205-217
12. Brooks, B.; Janezic, D.; Karplus, M. Harmonic Analysis of Large Systems-1. Methodology J. Comput. Chem. 1995, 16, 1522-1542
13. Janezic, D.; Venable, R. M.; Brooks, B. R. Harmonic Analysis of Large Systems-3. Comparison with Molecular Dynamics J. Comput. Chem. 1995, 16, 1554-1566
14. Reinhard, F.; Grubmueller, H. Estimation of Absolute Solvent and Solvation Shell Entropies via Permutation Reduction. J. Chem. Phys. 2007, 126.
15. Graziano, G. Hydration Entropy of Polar, Nonpolar and Charged Species Chem. Phys. Lett. 2009, 479, 56-59
16. Lazaridis, T. Inhomogeneous Fluid Approach to Solvation Thermodynamics. 1. Theory J. Phys. Chem. B 1998, 102, 3531-3541
17. Lazaridis, T. Inhomogeneous Fluid Approach to Solvation Thermodynamics. 2. Application to Simple Fluids J. Phys. Chem. B 1998, 102, 3542-3550
18. Lin, S.-T.; Maiti, P. K.; Goddard, W. A. Two-Phase Therodynamic Model for Efficient and Accurate Absolute Entropy of Water from Molecular Dynamics Simulations J. Phys. Chem. B 2010, 114, 8191-8198
19. Henchman, R. H. Free Energy of Liquid Water from a Computer Simulation via Cell Theory J. Chem. Phys. 2007, 126, 064504
20. Klefas-Stennett, M.; Henchman, R. H. Classical and Quantum Gibbs Free Energies and Phase Behavior of Water Using Simulation and Cell Theory J. Phys. Chem. B 2008, 112, 9769-9776
21. Lazaridis, T. Solvent Reorganization Energy and Entropy in Hydrophobic Hydration J. Phys. Chem. B 2000, 104, 4964-4979
22. Aqvist, J. Ion Water Interaction Potentials Derived from Free Energy Perturbation Simulations J. Phys. Chem. 1990, 94, 8021-8024
23. Bradbrook, G. M.; Gleichmann, T.; Harrop, S. J.; Habash, J.; Raftery, J.; Kalb, J.; Yariv, J.; Hillier, J. H.; Helliwell, J. R. X-ray and Molecular Dynamics Studies of Concanavalin-A Glucoside and Mannoside Complexes-Relating Structure to Thermodynamics of Binding J. Chem. Soc., Faraday Trans. 1998, 94, 1603-1611
24. Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. The Amber Biomolecular Simulation Programs J. Comput. Chem. 2005, 26, 1668-1688
25. Botev, Z. I.; Kroese, D. P. An Efficient Algorithm for Rare-Event Probability Estimation, Combinatorial Optimization and Counting Methodol. Comput. Appl. Probab. 2008, 10, 471-505
26. Mahoney, M. W.; Jorgensen, W. L. A Five-Site Model for Liquid Water and the Reproduction of the Density Anomaly by Rigid Nonpolarizable Potential Functions J. Chem. Phys. 2000, 112, 8910-8922
27. Kusalik, P. G.; Svishchev, I. M. The Spatial Structure in Liquid Water Science 1994, 265, 1219-1221
28. Horn, H. W.; Swope, W. C.; Pitera, J. W.; Madura, J. D.; Dick, T. J.; Hura, G. L.; Head-Gordon, T. Development of an Improved Four-Site Water Model for Biomolecular Simulations: TIP4P-Ew J. Chem. Phys. 2004, 120, 9665-9678
29. Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald-An n log(n) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089-10092
30. Feller, S.; Zhang, Y.; Pastor, R.; Brooks, B. Constant-Pressure Molecular Dynamics Simulation-The Langevin Piston Method J. Chem. Phys. 1995, 103, 4613-4621
31. Loeffler, H. H.; Rode, B. M. The Hydration Structure of the Lithium Ion J. Chem. Phys. 2002, 117, 110-117
32. Tongraar, A.; Liedl, K. R.; Rode, B. M. The Hydration Shell Structure of Li+ Investigated by Born-Oppenheimer Ab Initio QM/MM Dynamics Chem. Phys. Lett. 1998, 286, 56-64
33. Azam, S. S.; Hofer, T. S.; Randolf, B. R.; Rode, B. M. Hydration of Sodium(I) and Potassium(I) Revisited: A Comparative QM/MM and QMCF MD Simulation Study of Weakly Hydrated Ions J. Phys. Chem. A 2009, 113, 1827-1834
34. Tongraar, A.; Liedl, K. R.; Rode, B. M. Born-Oppenheimer Ab Initio QM/MM dynamics Simulations of Na+ and K+ in Water: From Structure Making to Structure Breaking Effects J. Phys. Chem. A 1998, 102, 10340-10347
35. Hofer, T. S.; Randolf, B. R.; Rode, B. M. Structure-Breaking Effects of Solvated Rb(I) in Dilute Aqueous Solution-An Ab Initio QM/MM MD Approach J. Comput. Chem. 2005, 26, 949-956
36. Schwenk, C. F.; Hofer, T. S.; Rode, B. M. Structure Breaking Effect of Hydrated Cs+ J. Phys. Chem. A 2004, 108, 1509-1514
37. Tongraar, A.; Rode, B. M. Structural Arrangement and Dynamics of the Hydrated Mg2+: An Ab Initio QM/MM Molecular Dynamics Simulation Chem. Phys. Lett. 2005, 409, 304-309
38. Sheather, S. J.; Jones, M. C. A Reliable Data-Based Bandwidth Selection Method for Kernel Density Estimation J. R. Stat. Soc. Methods B 1991, 53, 683-690
39. Bowman, A W. A Comparative Study of Some Kernel-Based Nonparametric Density Estimators J. Stat. Comput. Simul. 1985, 21, 313-327
40. Botev, Z. I.; Grotowski, J. F.; Kroese, D. P. Kernel Density Estimation via Diffusion Ann. Stat. 2010, 38, 2916-2957
41. Haar, A. Der Massbegriff in der Theorie der Kontinuierlichen Gruppen Ann. Math. 1933, 34, 147-169
42. Peschke, M.; Blades, A. T.; Kebarle, P. Hydration Energies and Entropies for Mg2+, Ca2+, Sr2+ and Ba2+ from Gas-Phase Ion-Water Molecule Equilibria Determinations J. Phys. Chem. A 1998, 102, 9978-9985
43. Noyes, R. Thermodynamics of Ion Hydration as a Measure of Effective Dielectric Properties of Water J. Am. Chem. Soc. 1962, 84, 513
44. Marcus, Y. Thermodynamic Functions of Transfer of Singe Ions from Water to Nonaqueous and Mixed Solvents. 2. Enthalpies and Entropies of Transfer to Nonaqueous Solvents Pure Appl. Chem. 1985, 57, 1103-1128
45. Botev, Z. I.; Kroese, D. P.; Taimre, T. Generalized Cross-Entropy Methods with Applications to Rare-Event Simulation and Optimization Simul.-Trans. Soc. Model. Simul. Int. 2007, 83, 785-806